Contacts of the helix formed by residues 729 - 760 (chain B) in PDB entry 3KZ1
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 729 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727B GLY 3.8 2.0 + - - -
728B LEU* 1.3 73.3 - - - +
730B GLN* 1.3 66.9 + - - +
731B ARG* 3.7 15.3 + - + +
732B GLU* 3.1 32.3 + - + +
733B ILE* 3.0 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B LEU 4.1 0.4 + - - -
729B THR* 1.3 74.9 + - - +
731B ARG* 1.3 65.7 + - - +
733B ILE* 3.0 24.0 + - - +
734B ASP* 2.9 44.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 731 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B THR* 3.4 12.4 + - + +
730B GLN* 1.3 77.4 - - - +
732B GLU* 1.3 59.6 + - + +
734B ASP* 3.2 11.9 + - - +
735B ARG* 2.9 25.8 + - - +
894B LYS 3.2 24.9 + - - -
895B HIS* 3.4 34.7 - - + +
896B THR 4.0 13.5 + - - +
897B GLU* 4.9 14.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 732 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B LEU* 4.3 23.6 - - + -
729B THR* 3.1 28.4 + - + +
731B ARG* 1.3 77.9 - - + +
733B ILE* 1.3 61.7 + - - +
735B ARG* 2.7 44.3 + - - +
736B GLN* 2.8 48.2 + - + +
805B ILE* 4.6 4.7 - - + +
806B ILE 4.4 0.2 - - - +
895B HIS 5.2 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 733 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B TRP* 4.6 12.6 - - + -
717B GLN* 3.9 35.0 - - + +
725B VAL* 4.7 15.5 - - + -
728B LEU* 3.8 31.6 - - + +
729B THR 3.2 24.7 - - - +
730B GLN* 3.0 25.5 + - - +
732B GLU* 1.3 75.4 - - - +
734B ASP* 1.3 67.9 + - - +
736B GLN* 3.2 6.5 + - - +
737B GLU* 3.0 27.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 734 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730B GLN* 2.9 44.3 + - - +
731B ARG* 3.6 8.4 - - - +
733B ILE* 1.3 79.1 - - - +
735B ARG* 1.3 60.6 + - - +
737B GLU* 3.4 10.4 + - - +
738B VAL* 3.2 27.0 + - - +
895B HIS* 3.6 31.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 735 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731B ARG 2.9 14.6 + - - +
732B GLU* 2.7 52.4 + - - +
733B ILE 3.1 0.2 - - - -
734B ASP* 1.3 75.4 - - - +
736B GLN* 1.3 75.5 + - - +
738B VAL* 3.4 5.0 + - - +
739B ILE* 3.1 39.5 + - + +
806B ILE 3.6 5.3 + - - -
807B LYS* 2.7 30.1 + - - +
808B GLU* 4.2 1.2 - - - +
809B ILE* 4.7 1.6 - - - +
892B ILE* 4.7 12.2 - - + +
895B HIS* 3.4 34.0 - - + +
896B THR* 4.2 15.1 + - - +
902B GLU* 4.0 19.2 + - - +
906B LEU* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 736 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
716B TRP* 3.5 46.4 + - + -
728B LEU* 5.2 1.6 - - + -
732B GLU* 2.8 43.1 + - + +
733B ILE 3.2 1.1 + - - +
735B ARG* 1.3 80.5 - - - +
737B GLU* 1.3 53.3 + - - +
739B ILE* 3.6 9.0 - - - +
740B ASN* 2.7 38.0 + - - +
804B PRO 4.2 0.2 - - - +
805B ILE* 3.6 14.9 - - + +
806B ILE* 2.9 52.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 737 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B ASN* 3.5 17.8 - - - +
716B TRP* 2.7 30.5 + - + +
717B GLN* 3.0 49.2 + - - +
733B ILE* 3.0 19.8 + - + +
734B ASP* 3.5 13.5 - - - +
735B ARG 3.2 0.2 - - - -
736B GLN* 1.3 76.0 - - - +
738B VAL* 1.3 60.0 + - + +
740B ASN* 3.6 3.5 + - - +
741B GLU* 3.1 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 738 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734B ASP 3.2 14.1 + - - +
735B ARG* 4.0 5.6 - - - +
737B GLU* 1.3 76.4 - - + +
739B ILE* 1.3 60.0 + - - +
741B GLU* 3.0 17.7 + - + +
742B LEU* 2.9 26.9 + - - +
888B LEU* 3.8 13.0 - - + +
891B SER* 3.7 32.1 - - - +
892B ILE* 3.5 28.5 - - + +
895B HIS* 4.3 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 739 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
735B ARG* 3.1 58.4 + - + +
736B GLN* 3.7 14.4 - - - +
738B VAL* 1.3 73.9 - - - +
740B ASN* 1.3 63.0 + - - +
742B LEU* 3.3 6.7 + - - +
743B PHE* 3.1 45.5 + - + -
806B ILE* 4.2 26.2 - - + -
809B ILE* 3.7 24.0 - - + -
892B ILE* 4.2 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 740 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
715B ASN 4.8 1.9 - - - -
716B TRP* 3.8 43.8 + - + +
719B THR* 5.3 1.2 + - - -
736B GLN 2.7 21.1 + - - +
737B GLU* 3.8 3.7 - - - +
739B ILE* 1.3 76.1 - - - +
741B GLU* 1.3 56.6 + - - +
743B PHE* 3.3 7.7 + - - +
744B VAL* 3.0 46.5 + - - +
800B ARG* 4.9 8.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 741 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737B GLU 3.1 12.9 + - - +
738B VAL* 3.0 21.7 + - + +
740B ASN* 1.3 73.0 + - - +
742B LEU* 1.3 56.8 + - - +
744B VAL* 5.0 2.5 - - - -
745B THR* 2.6 56.2 + - + +
884B LYS* 5.4 3.5 - - - +
888B LEU* 4.1 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 742 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
738B VAL 2.9 12.1 + - - +
739B ILE 3.6 7.0 - - - +
741B GLU* 1.3 78.2 - - - +
743B PHE* 1.3 64.6 + - + +
745B THR* 3.5 4.6 + - - -
746B GLU* 3.0 24.9 + - - +
792B TRP* 4.3 9.9 - - + -
796B MET* 4.1 16.2 - - + -
809B ILE* 4.5 6.5 - - + -
813B MET* 3.9 29.8 - - + -
817B PHE* 6.3 0.2 - - + -
881B ARG* 4.0 9.0 - - - +
885B TYR* 4.4 7.6 - - + -
888B LEU* 3.9 30.9 - - + +
889B LEU* 5.2 2.0 - - + -
892B ILE* 3.8 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 743 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739B ILE* 3.1 37.1 + - + +
740B ASN* 3.7 14.6 - - - +
742B LEU* 1.3 80.7 - - + +
744B VAL* 1.3 63.4 + - + +
746B GLU* 3.1 13.5 + - - +
747B ALA* 3.2 12.3 + - - +
793B CYS* 5.4 0.7 - - - -
796B MET* 3.4 65.7 - - + +
797B LYS* 5.7 0.4 - - - -
799B LEU* 4.6 4.3 - - + -
800B ARG* 5.1 8.5 - - + -
806B ILE* 4.6 19.7 - - + -
809B ILE* 4.0 16.4 - - + -
812B LEU* 4.0 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 744 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B ASN* 3.0 40.1 + - - +
741B GLU* 4.4 2.7 - - - +
743B PHE* 1.3 76.5 - - + +
745B THR* 1.3 61.5 + - + +
747B ALA* 3.3 9.1 + - + +
748B SER* 3.0 30.7 + - - +
29F GLN* 6.2 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B GLU* 2.6 44.7 + - + +
742B LEU* 3.5 3.5 + - - -
744B VAL* 1.3 78.8 - - + +
746B GLU* 1.3 57.1 + - - +
748B SER* 3.9 10.9 - - - +
749B HIS* 3.0 27.2 + - - +
881B ARG* 3.1 32.9 + - - -
888B LEU* 4.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
742B LEU 3.0 15.4 + - - +
743B PHE 3.1 10.5 + - - +
745B THR* 1.3 78.3 - - - +
747B ALA* 1.3 57.6 + - - +
749B HIS* 3.4 4.6 + - - +
750B LEU* 3.0 26.7 + - - +
789B HIS* 2.5 42.1 + - - +
792B TRP* 3.6 19.5 - - + -
793B CYS* 3.8 16.8 - - - -
796B MET* 3.8 20.4 - - + -
881B ARG* 3.2 15.6 + - - +
885B TYR* 2.7 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
743B PHE 3.2 9.1 + - - +
744B VAL* 3.3 10.3 + - + +
746B GLU* 1.3 77.4 - - - +
748B SER* 1.3 66.9 + - - +
750B LEU* 3.1 10.2 + - + +
751B ARG* 2.9 26.5 + - - +
793B CYS* 4.1 9.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 748 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A LYS* 6.1 3.4 - - - -
744B VAL* 3.0 24.5 + - - +
745B THR* 3.9 11.6 - - - +
747B ALA* 1.3 76.3 - - - +
749B HIS* 1.3 64.4 + - - +
751B ARG* 3.4 10.7 + - - +
752B THR* 3.1 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
745B THR 3.0 19.8 + - - +
746B GLU* 3.5 5.8 - - - +
747B ALA 3.1 0.2 - - - -
748B SER* 1.3 76.3 - - - +
750B LEU* 1.3 63.9 + - - +
752B THR* 3.0 19.2 + - - -
753B LEU* 3.2 30.5 + - + +
789B HIS* 3.6 24.1 + + - -
877B SER* 3.3 37.8 + - - -
878B GLU* 3.2 27.2 + - - -
881B ARG* 3.4 33.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 750 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746B GLU 3.0 15.1 + - - +
747B ALA* 3.1 13.2 + - - +
749B HIS* 1.3 78.1 + - - +
751B ARG* 1.3 64.8 + - + +
753B LEU* 3.2 11.5 + - + +
754B ARG* 3.1 52.2 + - - +
786B ILE* 4.0 18.6 - - + +
789B HIS* 3.9 10.5 - - + -
790B ASN* 3.6 34.3 - - + +
793B CYS* 4.2 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 751 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A LYS* 4.8 14.3 - - - +
747B ALA 2.9 23.4 + - - +
748B SER* 3.8 11.9 - - - +
750B LEU* 1.3 76.3 - - + +
752B THR* 1.3 52.9 + - - +
754B ARG* 3.0 12.3 + - + +
755B VAL* 2.7 52.2 + - + +
865B GLN* 2.8 40.3 + - - +
867B ARG* 2.7 38.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 752 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1040A LYS* 4.8 11.4 + - - -
748B SER* 3.1 15.1 + - - -
749B HIS* 3.0 13.9 + - - -
751B ARG* 1.3 77.0 + - - +
753B LEU* 1.3 55.9 + - - +
755B VAL* 3.4 9.0 + - - +
756B LEU* 3.0 28.8 + - + +
874B LEU* 3.8 32.2 - - + +
877B SER* 3.3 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 753 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
749B HIS* 3.2 39.4 + - + +
750B LEU* 3.2 9.4 + - + +
752B THR* 1.3 74.2 - - - +
754B ARG* 1.3 61.6 + - - +
756B LEU* 3.5 22.5 - - + +
757B ASP* 3.3 15.4 + - - +
782B LEU* 4.3 6.0 - - + +
785B LEU* 4.0 26.5 - - + +
786B ILE* 3.8 26.8 - - + +
789B HIS* 3.7 26.2 - - + -
832B PHE* 5.3 2.0 - - + -
877B SER* 5.1 6.5 - - - -
878B GLU* 3.8 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 754 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750B LEU* 3.1 40.8 + - + +
751B ARG* 3.0 14.3 + - + +
753B LEU* 1.3 75.2 - - - +
755B VAL* 1.3 60.9 + - + +
757B ASP* 3.1 7.6 + - - +
758B LEU* 2.9 32.0 + - - +
786B ILE* 3.6 29.7 - - + +
790B ASN* 3.7 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 755 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B ARG* 2.7 36.8 + - + +
752B THR* 3.6 9.0 - - + +
754B ARG* 1.3 69.0 - - - +
756B LEU* 1.3 67.1 + - - +
757B ASP 3.1 0.2 + - - -
758B LEU* 4.9 1.1 - - - -
759B ILE* 3.1 46.1 + - + +
760B PHE* 3.9 1.8 + - + -
865B GLN* 3.4 43.5 - - + +
866B CYS* 4.2 13.2 - - - -
874B LEU* 4.3 17.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 756 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752B THR* 3.0 19.4 + - + +
753B LEU* 3.5 27.8 - - + +
754B ARG 3.4 0.2 - - - -
755B VAL* 1.3 76.7 - - - +
757B ASP* 1.3 58.8 + - - +
760B PHE* 3.3 17.6 + - + +
761B TYR* 3.0 24.4 + - - +
779B PHE* 4.2 10.7 - - + -
782B LEU* 4.3 12.9 - - + +
832B PHE* 4.7 9.6 - - + -
871B LEU* 3.9 28.7 - - + -
874B LEU* 3.8 36.3 - - + +
875B ILE* 3.9 17.0 - - + +
877B SER* 5.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 757 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
753B LEU 3.3 9.8 + - - +
754B ARG* 3.1 9.0 + - - +
755B VAL 3.1 0.8 - - - -
756B LEU* 1.3 77.8 - - - +
758B LEU* 1.3 66.2 + - - +
761B TYR* 3.5 11.7 + - - -
762B GLN* 3.0 63.8 + - - +
782B LEU* 4.0 15.7 - - + +
783B PRO* 4.9 6.0 - - - +
786B ILE* 4.0 19.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 758 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
754B ARG 2.9 16.7 + - - +
755B VAL* 4.3 1.6 - - - +
757B ASP* 1.3 84.5 - - - +
759B ILE* 1.3 69.7 + - + +
762B GLN* 3.9 18.6 - - + +
763B ARG* 4.2 10.0 + - - +
865B GLN* 5.0 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 759 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B VAL* 3.1 32.2 + - + +
758B LEU* 1.3 89.6 - - + +
760B PHE* 1.3 66.0 + - + +
763B ARG* 3.7 30.4 + - - +
856B PHE* 4.8 0.9 - - - -
860B ALA* 3.5 32.6 - - - +
863B HIS* 3.9 24.9 - - + +
865B GLN* 3.3 37.0 - - + +
866B CYS* 4.0 10.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 760 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B VAL* 4.2 5.2 - - + -
756B LEU* 3.3 19.1 + - + +
759B ILE* 1.3 83.3 - - + +
761B TYR* 1.3 70.0 + - - +
762B GLN 3.3 1.8 - - - -
763B ARG* 3.1 4.0 + - - +
764B MET* 2.8 44.7 + - + +
779B PHE* 4.2 9.4 - - + -
856B PHE* 4.3 1.7 - + - -
857B MET* 4.1 9.9 - - - -
860B ALA* 3.7 23.8 - - + -
861B GLU* 4.0 18.2 - - + -
866B CYS* 3.7 29.2 - - - -
870B GLN 5.1 0.2 - - - -
871B LEU* 3.7 44.4 - - + -
874B LEU* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il